In 2375, Dougherty entered into an alliance with the Son'a, led by Ahdar Ru'afo, to covertly relocate the Ba'ku from a planet in the area of space known as "the Briar Patch," and then perform a procedure to collect metaphasic particles from the planet's rings. As this procedure would leave the planet uninhabitable, Dougherty and Ru'afo were forced to develop a plan whereby the Ba'ku would be transported to another planet using a holoship, leaving the Ba'ku completely unaware of what was transpiring. This would leave Dougherty and Ru'afo free to collect the particles, which had rejuvenating qualities, without killing the inhabitants. Although Dougherty had secured permission from the Federation Council to execute this mission, he actively attempted to prevent the details of the operation from reaching them, knowing that, if it were to be learned that the Federation had sanctioned the forced relocation of a peaceful people, public opinion would turn against him, and he would be unable to proceed.
Dougherty's plans were complicated, however, when the crew of the USS Enterprise uncovered the plot. As Captain Picard and members of his crew acted to protect the Ba'ku, Commander Riker, the Enterprise's first officer, attempted to reach the perimeter of the Briar Patch in order to contact the Council and inform them of the details of Dougherty's operation. Although Dougherty was initially reluctant, Ru'afo convinced him to let two Son'a battle cruisers intercept the Enterprise, explaining that, if the Federation were to learn the truth, the operation would be halted, and the Federation would lose an invaluable opportunity. Later, upon learning that the Son'a and the Ba'ku were, in actuality, the same race, and that the Son'a were simply attempting to gain revenge on those that had exiled them, Dougherty ordered Ru'afo to halt the operation, who responded by viciously beating Dougherty and restraining him in a device designed to stretch the flesh of one's face tighter. Dougherty then warned that if the operation goes ahead, the Federation would pursue the Son'a. Ru'afo responded that the Federation would never know what had transpired, before activating the device, killing Dougherty. (Star Trek: Insurrection)